Contacts of the strand formed by residues 524 - 529 (chain A) in PDB entry 1G88
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A TYR* 3.3 2.5 - - - -
329A PHE* 2.8 73.0 + + + +
331A MET 2.8 21.9 + - - -
502A ARG* 4.1 22.0 - - - -
503A MET 3.0 17.7 - - - +
504A SER* 3.7 8.1 - - - +
505A PHE* 4.6 2.7 - - - +
518A ILE* 3.4 33.4 + - + -
519A LYS* 3.8 22.7 - - + -
521A THR* 3.3 27.8 - - - +
523A CYS* 1.3 74.1 - - - +
525A ILE* 1.3 86.4 + - - +
526A GLU* 4.0 17.3 - - + -
370C VAL* 4.4 13.2 - - + -
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Residues in contact with ILE 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 3.5 26.9 - - + -
327A ALA 3.3 4.5 - - - -
328A TYR* 3.7 26.9 - - + -
350A VAL* 4.5 10.8 - - + -
362A PHE* 4.9 0.2 - - + -
364A LEU* 4.6 4.3 - - + -
387A VAL* 5.6 0.7 - - + -
389A LEU* 4.6 8.1 - - + -
502A ARG* 3.3 5.2 - - - +
503A MET* 2.8 59.2 + - + +
505A PHE* 4.3 19.1 - - + -
524A TRP* 1.3 88.2 - - - +
526A GLU* 1.3 60.2 + - - +
527A ILE* 3.9 17.3 + - + +
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Residues in contact with GLU 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A SER 3.7 2.4 - - - +
326A ILE* 3.6 1.9 - - - -
327A ALA* 2.9 34.8 + - + +
329A PHE* 3.9 26.2 - - + -
497A ARG* 4.7 1.9 + - - -
500A ILE* 3.6 21.0 - - + +
501A LEU 3.7 2.2 - - - -
502A ARG* 3.1 34.0 + - + -
524A TRP* 4.0 7.8 - - + -
525A ILE* 1.3 73.9 - - - +
527A ILE* 1.3 61.9 + - - +
528A HIS* 3.6 16.8 + - - +
368C SER* 2.9 35.7 + - - -
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Residues in contact with ILE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TRP* 5.7 1.3 - - + -
324A CYS* 4.2 21.3 - - + -
325A SER 3.7 4.0 - - - +
326A ILE* 4.2 8.7 - - + -
389A LEU* 3.4 39.5 - - + -
397A VAL* 6.2 1.3 - - + -
500A ILE* 3.3 6.5 - - - +
501A LEU* 2.7 59.7 + - + +
502A ARG* 5.2 0.7 - - - +
503A MET* 4.6 7.2 - - + -
525A ILE* 4.0 23.8 - - + +
526A GLU* 1.3 75.2 - - - +
528A HIS* 1.3 65.2 + - - +
529A LEU* 3.7 22.1 + - + +
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Residues in contact with HIS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A CYS* 3.0 26.3 - - - +
325A SER* 3.0 28.9 + - - +
499A CYS 4.3 2.2 - - - -
500A ILE* 3.4 26.8 - - + +
526A GLU* 3.6 19.6 + - - +
527A ILE* 1.3 72.9 - - - +
529A LEU* 1.3 62.9 + - - +
530A HIS* 3.5 7.8 - - + -
533A LEU* 4.0 20.6 - - + -
356C PRO* 6.2 0.4 - - + -
366C GLN* 3.3 36.8 + - + -
367C LEU* 4.5 2.8 + - + -
368C SER* 3.6 17.5 - - - -
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Residues in contact with LEU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TRP* 3.8 6.7 - - + +
324A CYS* 4.2 7.0 - - + -
395A GLY 5.3 1.3 - - - +
397A VAL* 4.1 17.0 - - + -
438A PHE* 3.7 43.1 - - + -
499A CYS 3.1 23.8 + - - +
501A LEU* 3.8 23.6 - - + -
527A ILE* 3.7 25.1 - - + +
528A HIS* 1.3 74.9 - - - +
530A HIS* 1.3 60.4 + - - +
531A ARG* 3.5 0.9 - - + +
532A ALA* 3.9 11.5 - - + +
533A LEU* 3.1 30.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il